Re: Spherical restraints

From: Almeida-HernŠndez, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Tue Apr 06 2021 - 10:50:11 CDT

Hi Giacomo,

Thank you for your reply. Yes, that was the problem.

The setting looks now like:

set config "

colvar {
  name LIG_sphere
  distance {
    group1 {atomNumbers 704} # Cu2+ cation
    group2 {atomNumbersRange 707-734} # Ligand
  }
}

harmonicWalls {
    colvars LIG_sphere
    outputEnergy on
    lowerWalls 0
    upperWalls 15
    forceConstant 1000
}
"

colvars on
cv config ${config}

Now, if I run it in my laptop it works well, but if I run it in a cluster with GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf > $INP.log), it writes -nan values:

TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674, 0.0173574/step, 4.39239 hours remaining, 672.355469 MB of memory in use.
ENERGY: 89000 nan 888064.2004 nan nan nan 0.0000 0.0000 0.0000 nan nan nan nan -nan nan nan nan nan nan nan

Any thoughts?

Best

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Tuesday, April 6, 2021 5:06:58 PM
To: NAMD list; Almeida-HernŠndez, Yasser, Dr.
Subject: Re: namd-l: Spherical restraints

Hello Yasser, there are a few things to check, but the first one would be to make sure that you actually loaded that configuration. There will be a (fairly verbose) set of messages printed when you do.

What you did there is setting a string variable "config" to contain the configuration text, which can be used in a Tcl script but you actually need to load it afterwards, e.g.:

cv config ${config}

On Tue, Apr 6, 2021 at 10:09 AM Almeida-HernŠndez, Yasser, Dr. <yasser.almeida-hernandez_at_uni-due.de<mailto:yasser.almeida-hernandez_at_uni-due.de>> wrote:

Hello,

I want to spherically restrain a ligand around a Cu2+ cation with harmonic walls. For this, I am using the colvars module as:

# Restraint the ligand in a sphere of r=15 AA around the Cu2+
set config "

colvars on

colvar {
  name LIG_sphere
  distance {
    group1 {atomNumbers 704} # Cu2+ cation
    group2 {atomNumbersRange 707-734} # Ligand
  }
}

harmonicWalls {
    name LIG_sphere
    colvars HL
    outputEnergy on
    lowerWalls 0
    upperWalls 15
    forceConstant 1000
}
"

.. but it doesn't work. The ligand tumbles all around.

Am I missing something? Any help will be appreciated.

Best,

Yasser

--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universitštsstr. 2, 45117 Essen
Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de>
Phone: +49 201 183 2457<tel:+49%20201%20183%202457>

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